Directed evolution has proved to be a powerful tool in protein engineering and synthetic biology. The most challenging part of directed evolution is typically the screening of mutants to assay for desired function. Many screening methods consist of simple binding assays, whereby a binding target is exposed to a mutant library, and mutants that do not wash away are selected. However, these assays are limited to the evolution of binding reagents, and a much wider space of applications is possible with directed evolution. For instance, it may be desirable to evolve gene circuits, genes for metabolic production of desired chemicals, genes for modifying or breaking down materials or chemicals, or components that regulate protein expression. Some of these applications have been addressed by other screening methods. These other screening methods have involved the expression of fluorescent or pigment proteins and subsequent screening based on fluorescence or color changes, use of fluorogenic or colorigenic enzyme substrates and subsequent screening based on fluorescence or color changes, expression of genes that regulate chemotaxis and subsequent screening based on spatial location of cells, or expression of genes that effect cell fitness and screening based on cell viability. In general, these methods are limited to either in vivo use or in vitro use, suffer from throughput or scalability issues, or lack broad applicability.
Therefore there remains a need in the art for methods of directed evolution screening that offer compatibility with in vivo and in vitro platforms (e.g. cells and cell-free systems), high throughput potential, scalability, and applicability to a broad range of different applications.